static internal Hashtable GetEqClassCollection()
{
SortedList rgClassToOneLetterAA = new SortedList();
foreach (string sThreeLetter in Biology.GetInstance().AminoAcidEquivalence.Keys)
{
char cAminoAcid = Biology.GetInstance().ThreeLetterAminoAcidAbbrevTo1Letter[sThreeLetter];
string sClass = Biology.GetInstance().AminoAcidEquivalence[sThreeLetter];
if (!rgClassToOneLetterAA.ContainsKey(sClass))
{
rgClassToOneLetterAA.Add(sClass, new StringBuilder());
}
StringBuilder aaList = (StringBuilder)rgClassToOneLetterAA[sClass];
aaList.Append(cAminoAcid);
}
Hashtable eqClassCollection = new Hashtable();
foreach (StringBuilder sb in rgClassToOneLetterAA.Values)
{
string s = sb.ToString();
foreach (char c in s)
{
eqClassCollection.Add(c, s);
}
}
return(eqClassCollection);
}
static public Biology GetInstance()
{
if (Singleton == null)
{
Singleton = new Biology();
}
return(Singleton);
}
public static IEnumerable <List <string> > EveryPropertyCombination(string aaSeq)
{
List <List <string> > propertyListList = new List <List <string> >();
foreach (char aa in aaSeq)
{
string aaAsString = Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[aa];
propertyListList.Add(KmerProperties.AaToPropList[aaAsString]);
}
return(SpecialFunctions.EveryCombination(propertyListList));
}
public static Set <char> PropertyNameToAASet(string propertyName)
{
KmerProperties kmerProperties = KmerProperties.GetInstance();
int propertyNum = kmerProperties.PropertyToNumber[propertyName];
Set <char> aaSet = Set <char> .GetInstance();
foreach (KeyValuePair <string, bool[]> aaAndBits in kmerProperties.AABits)
{
if (aaAndBits.Value[propertyNum])
{
char aa = Biology.GetInstance().ThreeLetterAminoAcidAbbrevTo1Letter[aaAndBits.Key];
aaSet.AddNew(aa);
}
}
return(aaSet);
}
//internal EpitopeLearningData[] Split(int cCrossValPart, Random aRandom)
//{
// List<KeyValuePair<MerAndHlaToLength, bool>> shuffleList = new List<KeyValuePair<MerAndHlaToLength, bool>>();
// foreach (KeyValuePair<Pair<string, Hla>, bool> merAndHlaToLengthWithLabel in this)
// {
// shuffleList.Add(merAndHlaToLengthWithLabel);
// int iRandomPos = aRandom.Next(shuffleList.Count);
// shuffleList[shuffleList.Count - 1] = shuffleList[iRandomPos];
// shuffleList[iRandomPos] = merAndHlaToLengthWithLabel;
// }
// EpitopeLearningData[] rgrg = new EpitopeLearningData[cCrossValPart];
// for (int irgrg = 0; irgrg < rgrg.Length; ++irgrg)
// {
// rgrg[irgrg] = new EpitopeLearningData(string.Format("{0}{1}", Name, irgrg));
// }
// for (int iShuffleList = 0; iShuffleList < shuffleList.Count; ++iShuffleList)
// {
// KeyValuePair<MerAndHlaToLength, bool> merAndHlaToLengthWithLabel = shuffleList[iShuffleList];
// int iSet = iShuffleList * cCrossValPart / shuffleList.Count;
// rgrg[iSet].Add(merAndHlaToLengthWithLabel.Key, merAndHlaToLengthWithLabel.Value);
// }
// return rgrg;
//}
public static EpitopeLearningData GetDbWhole(HlaFactory hlaFactory, int eLength, string datasetName, string fileOrResourceName)
{
Set <string> wantedSet = CreateSourceSet(datasetName);
EpitopeLearningData rg = new EpitopeLearningData(datasetName);
//SpecialFunctions.CheckCondition(hlaResolution.Equals(HlaResolution.ABMixed));
foreach (Dictionary <string, string> row in Predictor.TabFileTable(fileOrResourceName, "peptide hla source label", false))
{
string peptide = row["peptide"];
SpecialFunctions.CheckCondition(Biology.GetInstance().LegalPeptide(peptide), string.Format("Peptide, '{0}', contains illegal char.", peptide));
if (peptide.Length != eLength) //!!!const
{
continue;
}
string source = row["source"];
Set <string> providedSet = CreateSourceSet(source);
//Debug.Assert(providedSet.IsSubsetOf(Set<string>.GetInstance(new string[] { "Aplus", "LANL", "IEDB" }))); // real assert
if (providedSet.IntersectionIsEmpty(wantedSet))
{
continue;
}
Hla hla = hlaFactory.GetGroundInstance(row["hla"]);
//HlaToLength hlaToLength = HlaToLength.GetInstance(hla, hlaResolution);
Pair <string, Hla> peptideAndHla = new Pair <string, Hla>(peptide, hla);
//MerAndHlaToLength aMerAndHlaToLength = MerAndHlaToLength.GetInstance(peptide, hlaToLength, kmerDefinition);
string label = row["label"];
SpecialFunctions.CheckCondition(label == "0" || label == "1", string.Format("Warning: Epitope example {0} has unknown label {1} and will be ignored.", peptideAndHla, label));
rg[peptideAndHla] = (label == "1");
}
return(rg);
}
public static Dictionary <string, List <string> > CreateAAToPropList()
{
Dictionary <string, List <string> > aaToPropList = new Dictionary <string, List <string> >();
foreach (string aa in Biology.GetInstance().AminoAcidCollection.Keys)
{
if (aa == "STOP" || aa == "DELETE")
{
continue;
}
bool[] rgsBit = KmerProperties.GetInstance().AABits[aa];
List <string> probList = new List <string>();
for (int iProperty = 0; iProperty < rgsBit.Length; ++iProperty)
{
if (rgsBit[iProperty])
{
string property = KmerProperties.GetInstance().AAPropertyCollection[iProperty];
probList.Add(property);
}
}
aaToPropList.Add(aa, probList);
}
return(aaToPropList);
}
private void ReadFile()
{
for (HowConsevered howConsevered = HowConsevered.Conserved; howConsevered <= HowConsevered.SemiConserved; ++howConsevered)
{
HowConseveredToForward[(int)howConsevered] = new SortedList();
HowConseveredToBackward[(int)howConsevered] = new SortedList();
}
string inputFileName = @"SimilarityOfAminoAcids.txt";
SortedList rgHeadings = new SortedList();
using (StreamReader streamreaderInputFile = Predictor.OpenResource(inputFileName))
{
string sLine;
char cPrevHeading = '\0';
while (null != (sLine = streamreaderInputFile.ReadLine()))
{
if (sLine.StartsWith("//"))
{
continue;
}
//There must be a line for every amino acid and they must be in alpha order
string[] tableParts = sLine.Split(' '); //!!!const
SpecialFunctions.CheckCondition(tableParts.Length == 3); //!!!raise error
Debug.Assert(tableParts[0].Length > 0);
char cHeading = tableParts[0][0];
SpecialFunctions.CheckCondition(cPrevHeading < cHeading); //!!!raise error
cPrevHeading = cHeading;
SpecialFunctions.CheckCondition(Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter.ContainsKey(cHeading)); //!!!raise error
SpecialFunctions.CheckCondition(!rgHeadings.ContainsKey(cHeading)); //!!!raise error
rgHeadings.Add(cHeading, null);
//We must see every amino acid in the line;
SortedList rgInLine = new SortedList();
foreach (string part in tableParts)
{
foreach (char cAA in part)
{
SpecialFunctions.CheckCondition(Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter.ContainsKey(cAA)); //!!!raise error
SpecialFunctions.CheckCondition(!rgInLine.ContainsKey(cAA)); //!!!raise error
rgInLine.Add(cAA, null);
}
}
SpecialFunctions.CheckCondition(rgInLine.Count == 20); //!!!raise error
foreach (char cAA in tableParts[(int)HowConsevered.Conserved])
{
AddPair(cHeading, cAA, HowConsevered.Conserved);
AddPair(cHeading, cAA, HowConsevered.SemiConserved);
}
foreach (char cAA in tableParts[(int)HowConsevered.SemiConserved])
{
AddPair(cHeading, cAA, HowConsevered.SemiConserved);
}
}
}
SpecialFunctions.CheckCondition(rgHeadings.Count == 20); //!!!raise error
}